dadded v2 of barplot layput
This commit is contained in:
parent
da8f8d90d4
commit
7c40e13771
7 changed files with 800 additions and 79 deletions
292
scripts/plotting/plotting_thesis/basic_barplots2.R
Normal file
292
scripts/plotting/plotting_thesis/basic_barplots2.R
Normal file
|
|
@ -0,0 +1,292 @@
|
|||
#!/usr/bin/env Rscript
|
||||
#########################################################
|
||||
# TASK: Barplots for mCSM DUET, ligand affinity, and foldX
|
||||
# basic barplots with count of mutations
|
||||
# basic barplots with frequency of count of mutations
|
||||
|
||||
# , df_colname = ""
|
||||
# , leg_title = ""
|
||||
# , ats = 25 # axis text size
|
||||
# , als = 22 # axis label size
|
||||
# , lts = 20 # legend text size
|
||||
# , ltis = 22 # label title size
|
||||
# , geom_ls = 10 # geom_label size
|
||||
# , yaxis_title = "Number of nsSNPs"
|
||||
# , bp_plot_title = ""
|
||||
# , label_categories = c("Destabilising", "Stabilising")
|
||||
# , title_colour = "chocolate4"
|
||||
# , subtitle_text = NULL
|
||||
# , sts = 20
|
||||
# , subtitle_colour = "pink"
|
||||
# #, leg_position = c(0.73,0.8) # within plot area
|
||||
# , leg_position = "top"
|
||||
# , bar_fill_values = c("#F8766D", "#00BFC4")
|
||||
#########################################################
|
||||
#=============
|
||||
# Data: Input
|
||||
#==============
|
||||
#source("~/git/LSHTM_analysis/config/alr.R")
|
||||
source("~/git/LSHTM_analysis/config/embb.R")
|
||||
#source("~/git/LSHTM_analysis/config/katg.R")
|
||||
#source("~/git/LSHTM_analysis/config/gid.R")
|
||||
#source("~/git/LSHTM_analysis/config/pnca.R")
|
||||
#source("~/git/LSHTM_analysis/config/rpob.R")
|
||||
|
||||
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
|
||||
source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
|
||||
|
||||
class(merged_df3)
|
||||
merged_df3 = as.data.frame(merged_df3)
|
||||
|
||||
class(df3)
|
||||
head(merged_df3$pos_count)
|
||||
|
||||
nc_pc_CHANGE = which(colnames(merged_df3)== "pos_count"); nc_pc_CHANGE
|
||||
colnames(merged_df3)[nc_pc_CHANGE] = "df2_pos_count_all"
|
||||
head(merged_df3$pos_count)
|
||||
head(merged_df3$df2_pos_count_all)
|
||||
|
||||
# DROP pos_count column
|
||||
# merged_df3$pos_count <-NULL
|
||||
merged_df3 = merged_df3[, !colnames(merged_df3)%in%c("pos_count")]
|
||||
head(merged_df3$pos_count)
|
||||
|
||||
df3 = merged_df3[, colnames(merged_df3)%in%plotting_cols]
|
||||
|
||||
|
||||
#=======
|
||||
# output
|
||||
#=======
|
||||
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
|
||||
cat("plots will output to:", outdir_images)
|
||||
|
||||
###########################################################
|
||||
#------------------------------
|
||||
# plot default sizes
|
||||
#------------------------------
|
||||
#=========================
|
||||
# Affinity outcome
|
||||
# check this var: outcome_cols_affinity
|
||||
# get from preformatting or put in globals
|
||||
#==========================
|
||||
DistCutOff
|
||||
LigDist_colname # = "ligand_distance" # from globals
|
||||
ppi2Dist_colname
|
||||
naDist_colname
|
||||
|
||||
###########################################################
|
||||
# get plotting data within the distance
|
||||
df3_lig = df3[df3[[LigDist_colname]]<DistCutOff,]
|
||||
df3_ppi2 = df3[df3[[ppi2Dist_colname]]<DistCutOff,]
|
||||
df3_na = df3[df3[[naDist_colname]]<DistCutOff,]
|
||||
common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol)
|
||||
|
||||
#------------------------------
|
||||
# barplot for ligand affinity:
|
||||
# <10 Ang of ligand
|
||||
#------------------------------
|
||||
mLigP = stability_count_bp(plotdf = df3_lig
|
||||
, df_colname = "ligand_outcome"
|
||||
#, leg_title = "mCSM-lig"
|
||||
#, bp_plot_title = paste(common_bp_title, "ligand")
|
||||
, yaxis_title = "Number of nsSNPs"
|
||||
, leg_position = "none"
|
||||
, subtitle_text = "mCSM-lig"
|
||||
, bar_fill_values = c("#F8766D", "#00BFC4")
|
||||
, subtitle_colour= "black"
|
||||
, sts = 10
|
||||
, lts = 8
|
||||
, ats = 12
|
||||
, als = 11
|
||||
, ltis = 11
|
||||
, geom_ls = 2.5)
|
||||
mLigP
|
||||
#------------------------------
|
||||
# barplot for ligand affinity:
|
||||
# <10 Ang of ligand
|
||||
# mmCSM-lig: will be the same no. of sites but the effect will be different
|
||||
#------------------------------
|
||||
mmLigP = stability_count_bp(plotdf = df3_lig
|
||||
, df_colname = "mmcsm_lig_outcome"
|
||||
#, leg_title = "mmCSM-lig"
|
||||
#, label_categories = labels_mmlig
|
||||
#, bp_plot_title = paste(common_bp_title, "ligand")
|
||||
|
||||
, yaxis_title = ""
|
||||
, leg_position = "none"
|
||||
, subtitle_text = "mmCSM-lig"
|
||||
, bar_fill_values = c("#F8766D", "#00BFC4")
|
||||
, subtitle_colour= "black"
|
||||
, sts = 10
|
||||
, lts = 8
|
||||
, ats = 12
|
||||
, als = 11
|
||||
, ltis = 11
|
||||
, geom_ls = 2.5
|
||||
)
|
||||
mmLigP
|
||||
#------------------------------
|
||||
# barplot for ppi2 affinity
|
||||
# <10 Ang of interface
|
||||
#------------------------------
|
||||
ppi2P = stability_count_bp(plotdf = df3_ppi2
|
||||
, df_colname = "mcsm_ppi2_outcome"
|
||||
#, leg_title = "mCSM-ppi2"
|
||||
#, label_categories = labels_ppi2
|
||||
#, bp_plot_title = paste(common_bp_title, "PP-interface")
|
||||
|
||||
, yaxis_title = "Number of nsSNPs"
|
||||
, leg_position = "none"
|
||||
, subtitle_text = "mCSM-ppi2"
|
||||
, bar_fill_values = c("#F8766D", "#00BFC4")
|
||||
, subtitle_colour= "black"
|
||||
, sts = 10
|
||||
, lts = 8
|
||||
, ats = 12
|
||||
, als = 11
|
||||
, ltis = 11
|
||||
, geom_ls = 2.5
|
||||
)
|
||||
ppi2P
|
||||
#####################################################################
|
||||
|
||||
# ------------------------------
|
||||
# bp site site count: mCSM-lig
|
||||
# < 10 Ang ligand
|
||||
# ------------------------------
|
||||
common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol)
|
||||
|
||||
posC_lig = site_snp_count_bp(plotdf = df3_lig
|
||||
, df_colname = "position"
|
||||
, xaxis_title = "Number of nsSNPs"
|
||||
, yaxis_title = "Number of Sites"
|
||||
, subtitle_colour = "chocolate4"
|
||||
, subtitle_text = ""
|
||||
, subtitle_size = 8
|
||||
, geom_ls = 2.6
|
||||
, leg_text_size = 10
|
||||
, axis_text_size = 10
|
||||
, axis_label_size = 10)
|
||||
|
||||
posC_lig
|
||||
# ------------------------------
|
||||
# bp site site count: ppi2
|
||||
# < 10 Ang interface
|
||||
# ------------------------------
|
||||
|
||||
posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2
|
||||
, df_colname = "position"
|
||||
, xaxis_title = "Number of nsSNPs"
|
||||
, yaxis_title = "Number of Sites"
|
||||
, subtitle_colour = "chocolate4"
|
||||
, subtitle_text = ""
|
||||
, subtitle_size = 8
|
||||
, geom_ls = 2.6
|
||||
, leg_text_size = 10
|
||||
, axis_text_size = 10
|
||||
, axis_label_size = 10)
|
||||
posC_ppi2
|
||||
#===============================================================
|
||||
# PE count
|
||||
rects <- data.frame(x = 1:6,
|
||||
colors = c("#ffd700" #gold
|
||||
, "#f0e68c" #khaki
|
||||
, "#da70d6"# orchid
|
||||
, "#ff1493"# deeppink
|
||||
, "#00BFC4" #, "#007d85" #blue
|
||||
, "#F8766D" )# red,
|
||||
)
|
||||
rects
|
||||
|
||||
rects$text = c("-ve Lig affinty"
|
||||
, "+ve Lig affinity"
|
||||
, "+ve PPI2 affinity"
|
||||
, "-ve PPI2 affinity"
|
||||
, "+ve stability"
|
||||
, "-ve stability")
|
||||
|
||||
# FOR EMBB ONLY
|
||||
rects$numbers = c(38, 0, 22, 9, 108, 681)
|
||||
rects$num_labels = paste0("n=", rects$numbers)
|
||||
|
||||
rects
|
||||
|
||||
#https://stackoverflow.com/questions/47986055/create-a-rectangle-filled-with-text
|
||||
|
||||
peP = ggplot(rects, aes(x, y = 0, fill = colors, label = paste0(text,"\n", num_labels))) +
|
||||
geom_tile(width = 1, height = 1) + # make square tiles
|
||||
geom_text(color = "black", size = 1.7) + # add white text in the middle
|
||||
scale_fill_identity(guide = "none") + # color the tiles with the colors in the data frame
|
||||
coord_fixed() + # make sure tiles are square
|
||||
coord_flip()+ scale_x_reverse() +
|
||||
# theme_void() # remove any axis markings
|
||||
theme_nothing() # remove any axis markings
|
||||
|
||||
|
||||
peP2 = ggplot(rects, aes(x, y = 0, fill = colors, label = paste0(text,"\n", num_labels))) +
|
||||
geom_tile() + # make square tiles
|
||||
geom_text(color = "black", size = 1.6) + # add white text in the middle
|
||||
scale_fill_identity(guide = "none") + # color the tiles with the colors in the data frame
|
||||
coord_fixed() + # make sure tiles are square
|
||||
theme_nothing() # remove any axis markings
|
||||
|
||||
|
||||
# ------------------------------
|
||||
# bp site site count: ALL
|
||||
# <10 Ang ligand
|
||||
# ------------------------------
|
||||
posC_all = site_snp_count_bp(plotdf = df3
|
||||
, df_colname = "position"
|
||||
, xaxis_title = "Number of nsSNPs"
|
||||
, yaxis_title = "Number of Sites"
|
||||
, subtitle_colour = "chocolate4"
|
||||
, subtitle_text = "All mutations sites"
|
||||
, subtitle_size = 8
|
||||
, geom_ls = 2.6
|
||||
, leg_text_size = 10
|
||||
, axis_text_size = 10
|
||||
, axis_label_size = 10)
|
||||
|
||||
##################################################################
|
||||
|
||||
#------------------------------
|
||||
# barplot for sensitivity:
|
||||
#------------------------------
|
||||
senP = stability_count_bp(plotdf = df3
|
||||
, df_colname = "sensitivity"
|
||||
#, leg_title = "mCSM-ppi2"
|
||||
#, label_categories = labels_ppi2
|
||||
#, bp_plot_title = paste(common_bp_title, "PP-interface")
|
||||
|
||||
, yaxis_title = "Number of nsSNPs"
|
||||
, leg_position = "none"
|
||||
, subtitle_text = "Sensitivity"
|
||||
, bar_fill_values = c("red", "blue")
|
||||
, subtitle_colour= "black"
|
||||
, sts = 10
|
||||
, lts = 8
|
||||
, ats = 12
|
||||
, als = 11
|
||||
, ltis = 11
|
||||
, geom_ls = 2.5
|
||||
)
|
||||
|
||||
|
||||
consurfP = stability_count_bp(plotdf = df3
|
||||
, df_colname = "consurf_outcome"
|
||||
#, leg_title = "ConSurf"
|
||||
#, label_categories = labels_consurf
|
||||
, yaxis_title = "Number of nsSNPs"
|
||||
, leg_position = "top"
|
||||
, subtitle_text = "ConSurf"
|
||||
, bar_fill_values = consurf_colours # from globals
|
||||
, subtitle_colour= "black"
|
||||
, sts = 10
|
||||
, lts = 8
|
||||
, ats = 12
|
||||
, als = 11
|
||||
, ltis = 11
|
||||
, geom_ls = 2.5)
|
||||
|
||||
consurfP
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue